Puente, president of Apecafe in El Salvador, a cooperative of more than 400 coffee farmers, has been watching closely as "la roya," a fungus, has devastated coffee plantations across Central America this year.

"We think outbreaks of violence and famine can occur in some cooperatives as a result of this situation," Puente said in a recent interview from San Salvador, where Apecafe is headquartered.

The price of coffee has yet to go up in the United States as a result of the fungus, also known as coffee rust disease. But Lindsey Bolger, senior director of coffee for Green Mountain Coffee Roasters here, said that could change next year.

"The consumer should be worried about the long-term implications of rust because it could severely limit the depth and breadth of coffee they love," Bolger said. "I can tell you as we have more and more episodes like this, your choices as a consumer could be compromised, and if we have enough of these episodes, the price will be impacted, along with quality."

Green Mountain Coffee is one of the biggest buyers of coffee in the world, purchasing some 207 million pounds in 2012. Bolger said the coffee market hasn't responded to Central American production dropping by 20% this year because Brazil, the biggest coffee grower in the world, is expected to bring in a good crop.

"I think the situation will be very different next year, because despite a bumper crop from Brazil, if coffee rust continues to be an issue, and plants in Central America are weakened, production will be down even more than 20%," Bolger said.

Puente says la roya has affected more than 74% of coffee plantations in El Salvador in the past year. He says the country will lose 1 million of the 1.7 million quintales of coffee beans it normally produces. One quintal is equal to about 100 pounds.

"The reality is we have been hit by something very powerful," Puente said. "The other issue is migration. People are going to want to move to the United States and other countries where they can find food."

La roya is hitting countries that produce arabica beans that real coffee drinkers insist upon, Bolger says. Together with Colombia, Central American countries produce about half the arabica beans in the world.

The International Coffee Organization (ICO), based in London, issued a report on la roya in May, saying more than 50% of the total coffee-growing areas in Central America have been affected. El Salvador, where Puente runs his cooperative, has the highest incidence rate of 74%, followed by Guatemala, at 70%, Costa Rica, at 64%, Nicaragua, at 37% and Honduras, at 25%.

The ICO estimates total damage this year of 2.7 million bags of coffee, a loss of about $500 million.

But the most troubling conclusion of the ICO report is the expectation that the impact of la roya will be "even more severe" next year.

Rick Peyser, director of social advocacy at Green Mountain Coffee, said an agronomist he spoke to in Guatemala in February backed up the conclusion of the ICO report.

"He said he felt in that area farmers would lose 60% to 80% of the crop next year," Peyser said. "This year, la roya came in toward the end of the harvest. Most of the harvest came in. But next year, these plants will be struggling."